I avoid having "user data" on local storage, using network filesystems for such. For Amiga systems where using networked filesystems is impractical, I use rsync to keep local directories in sync with remote directories. For the OS, I typically have a backup boot partition that is identical to the default boot partition, and also a stripped down plain OS boot partition that is barely ever touched, and disabled except from cold boots, for those foobar moments

Oh, and I also keep scripts and various (kickstarts and other OS components) updated around the crowd using a combination of rsync and git.